This isn't an upset but for me the worst Tony moment of all time was when they cut Elaine Stritch's speech in 2002. I mean just how wicked are the director's of the Tony Awards. I mean this woman poured her soul out to an auience and gave a legendary performance. For shame on them!
As other have said, I don't think everyone gets the definition of an upset. Avenue Q over Wicked was an upset; Spamalot over Piazza wasnt. While Piazza (or anything else, for that matter) is the better show, Spamalot was expected to win. Not an upset. The same is true for Lion King/Ragtime.
As for Music Man/WSS, they are both great shows. Really, this one could have gone either way, and people would still be complaining. That's the type of battle the Best Musical Tony should be every year.